Quantcast

I ask for your generous help regarding WebGBrowse

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

I ask for your generous help regarding WebGBrowse

Abraham Darius Llave IRRI
Good day!

I am Abraham Darius Llave, from the Bioinformatics Team of the C4 Rice Center,a department of the International Rice Research Institute.
I was tasked to try out GBrowse and in the process, I stumbled upon your tool WebGbrowse. I decided this is an essential addition to GBrowse as
I see that this streamlines processes our scientists are doing.

However though, configuring it is not smooth sailing.

First of all, my Apache's www-root is at

/var/www

GBrowse is accessible over the web at

http://localhost/gbrowse

Web

Other pertinent info from the file "WebGB.pm"
----------
our $TMP = '/usr/lib/tmp';
our $YAML_LIB = '/usr/lib/files/yamlib';
our $SEND_MAIL = '/usr/sbin/sendmail';
our $CONF = '';
our $WWW = '/var/www';
our $WWW2 = '/var/www/gbrowse2';
our $CONF2 = '/etc/gbrowse2';
---------

WebGbrowse installation is at

/var/www/webgbrowse


1) i get this error, in the logs:
-------------

[Wed Jan 30 16:44:53 2013] [error] [client 127.0.0.1] File does not exist: /var/www/include/img, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

------------
Is there some area in the scripts that I can adjust so that it doesn't search at /var/www/ for  include/img ? My band-aid solution for now is creating a symbolic link, i.e.:

ln -s /var/www/include /var/www/webgbrowse/include


2) Another error, which I really can't find a solution, thus knocking at your inboxes.. :D

----------
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Unable to open conf file /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf at /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50., referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Premature end of script headers: generateConfigurationData2.0, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
--------------
I can't find where between cgi-bin/webgbrowse/configureTracks and /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 files like /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf are supposedly created. Maybe you could provide me insight on that?

Thank you very much for taking the time to attending to my little inquiry.

Cheers,
--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone except as permitted by the author sender.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: I ask for your generous help regarding WebGBrowse

Scott Cain
Hi Abraham,

I don't really know, since I haven't installed WebGBrowse in a few years, but I wonder what the $CONF variable is supposed to be set to?  Perhaps that is the WebGBrowse configuration directory, and since it is empty, it doesn't have a place to create the configuration files.  Perhaps that would fix both problems.

Scott


On Wed, Jan 30, 2013 at 4:22 AM, Abraham Darius Llave (IRRI) <[hidden email]> wrote:
Good day!

I am Abraham Darius Llave, from the Bioinformatics Team of the C4 Rice Center,a department of the International Rice Research Institute.
I was tasked to try out GBrowse and in the process, I stumbled upon your tool WebGbrowse. I decided this is an essential addition to GBrowse as
I see that this streamlines processes our scientists are doing.

However though, configuring it is not smooth sailing.

First of all, my Apache's www-root is at

/var/www

GBrowse is accessible over the web at

http://localhost/gbrowse

Web

Other pertinent info from the file "WebGB.pm"
----------
our $TMP = '/usr/lib/tmp';
our $YAML_LIB = '/usr/lib/files/yamlib';
our $SEND_MAIL = '/usr/sbin/sendmail';
our $CONF = '';
our $WWW = '/var/www';
our $WWW2 = '/var/www/gbrowse2';
our $CONF2 = '/etc/gbrowse2';
---------

WebGbrowse installation is at

/var/www/webgbrowse


1) i get this error, in the logs:
-------------

[Wed Jan 30 16:44:53 2013] [error] [client 127.0.0.1] File does not exist: /var/www/include/img, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

------------
Is there some area in the scripts that I can adjust so that it doesn't search at /var/www/ for  include/img ? My band-aid solution for now is creating a symbolic link, i.e.:

ln -s /var/www/include /var/www/webgbrowse/include


2) Another error, which I really can't find a solution, thus knocking at your inboxes.. :D

----------
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Unable to open conf file /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf at /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50., referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Premature end of script headers: generateConfigurationData2.0, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
--------------
I can't find where between cgi-bin/webgbrowse/configureTracks and /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 files like /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf are supposedly created. Maybe you could provide me insight on that?

Thank you very much for taking the time to attending to my little inquiry.

Cheers,
--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone except as permitted by the author sender.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: I ask for your generous help regarding WebGBrowse

Ram Podicheti-2

Scott,

There is no need to set the $CONF variable as it was intended to point to the conf folder only if you have GBrowse 1.x. I am trying to figure out what might have went wrong (it has been quite a while since I last looked at the code). But, one thing I suspect is the permissions to write to /etc/gbrowse2.

 

Abraham, can you let me know where your GBrowse.conf file is located?

Thanks,

 

Ram

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, January 31, 2013 3:34 PM
To: Abraham Darius Llave (IRRI)
Cc: [hidden email]
Subject: Re: [Gmod-webgbrowse] I ask for your generous help regarding WebGBrowse

 

Hi Abraham,

I don't really know, since I haven't installed WebGBrowse in a few years, but I wonder what the $CONF variable is supposed to be set to?  Perhaps that is the WebGBrowse configuration directory, and since it is empty, it doesn't have a place to create the configuration files.  Perhaps that would fix both problems.

Scott

On Wed, Jan 30, 2013 at 4:22 AM, Abraham Darius Llave (IRRI) <[hidden email]> wrote:

Good day!

I am Abraham Darius Llave, from the Bioinformatics Team of the C4 Rice Center,a department of the International Rice Research Institute.
I was tasked to try out GBrowse and in the process, I stumbled upon your tool WebGbrowse. I decided this is an essential addition to GBrowse as
I see that this streamlines processes our scientists are doing.

However though, configuring it is not smooth sailing.

First of all, my Apache's www-root is at

/var/www

GBrowse is accessible over the web at

http://localhost/gbrowse

Web

Other pertinent info from the file "WebGB.pm"
----------
our $TMP = '/usr/lib/tmp';
our $YAML_LIB = '/usr/lib/files/yamlib';
our $SEND_MAIL = '/usr/sbin/sendmail';
our $CONF = '';
our $WWW = '/var/www';
our $WWW2 = '/var/www/gbrowse2';
our $CONF2 = '/etc/gbrowse2';

---------

WebGbrowse installation is at

/var/www/webgbrowse


1) i get this error, in the logs:
-------------

[Wed Jan 30 16:44:53 2013] [error] [client 127.0.0.1] File does not exist: /var/www/include/img, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

------------
Is there some area in the scripts that I can adjust so that it doesn't search at /var/www/ for  include/img ? My band-aid solution for now is creating a symbolic link, i.e.:

ln -s /var/www/include /var/www/webgbrowse/include


2) Another error, which I really can't find a solution, thus knocking at your inboxes.. :D

----------
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Unable to open conf file /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf at /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50., referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Premature end of script headers: generateConfigurationData2.0, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

--------------
I can't find where between cgi-bin/webgbrowse/configureTracks and /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 files like /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf are supposedly created. Maybe you could provide me insight on that?

Thank you very much for taking the time to attending to my little inquiry.

Cheers,
--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643

+639183981185

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone except as permitted by the author sender.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: I ask for your generous help regarding WebGBrowse

Abraham Darius Llave IRRI
Hello Scott and Ram! Thanks for responding!

Anyway, I have already figured it out and like what Scott said, the problem was because of the permissions in writing to /etc/gbrowse2 . It was my fault too that I misunderstood that the script was accessing a supposedly pre-created file when in fact it was opening such a file for writing.

Thank you again. Have a nice day!

On Fri, Feb 1, 2013 at 4:43 AM, Podicheti, Ram <[hidden email]> wrote:

Scott,

There is no need to set the $CONF variable as it was intended to point to the conf folder only if you have GBrowse 1.x. I am trying to figure out what might have went wrong (it has been quite a while since I last looked at the code). But, one thing I suspect is the permissions to write to /etc/gbrowse2.

 

Abraham, can you let me know where your GBrowse.conf file is located?

Thanks,

 

Ram

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, January 31, 2013 3:34 PM
To: Abraham Darius Llave (IRRI)
Cc: [hidden email]
Subject: Re: [Gmod-webgbrowse] I ask for your generous help regarding WebGBrowse

 

Hi Abraham,

I don't really know, since I haven't installed WebGBrowse in a few years, but I wonder what the $CONF variable is supposed to be set to?  Perhaps that is the WebGBrowse configuration directory, and since it is empty, it doesn't have a place to create the configuration files.  Perhaps that would fix both problems.

Scott

On Wed, Jan 30, 2013 at 4:22 AM, Abraham Darius Llave (IRRI) <[hidden email]> wrote:

Good day!

I am Abraham Darius Llave, from the Bioinformatics Team of the C4 Rice Center,a department of the International Rice Research Institute.
I was tasked to try out GBrowse and in the process, I stumbled upon your tool WebGbrowse. I decided this is an essential addition to GBrowse as
I see that this streamlines processes our scientists are doing.

However though, configuring it is not smooth sailing.

First of all, my Apache's www-root is at

/var/www

GBrowse is accessible over the web at

http://localhost/gbrowse

Web

Other pertinent info from the file "WebGB.pm"
----------
our $TMP = '/usr/lib/tmp';
our $YAML_LIB = '/usr/lib/files/yamlib';
our $SEND_MAIL = '/usr/sbin/sendmail';
our $CONF = '';
our $WWW = '/var/www';
our $WWW2 = '/var/www/gbrowse2';
our $CONF2 = '/etc/gbrowse2';

---------

WebGbrowse installation is at

/var/www/webgbrowse


1) i get this error, in the logs:
-------------

[Wed Jan 30 16:44:53 2013] [error] [client 127.0.0.1] File does not exist: /var/www/include/img, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

------------
Is there some area in the scripts that I can adjust so that it doesn't search at /var/www/ for  include/img ? My band-aid solution for now is creating a symbolic link, i.e.:

ln -s /var/www/include /var/www/webgbrowse/include


2) Another error, which I really can't find a solution, thus knocking at your inboxes.. :D

----------
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Unable to open conf file /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf at /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50., referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640
[Wed Jan 30 16:47:43 2013] [error] [client 127.0.0.1] Premature end of script headers: generateConfigurationData2.0, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=225c87610282ae0c1575dfb7e22bb640

--------------
I can't find where between cgi-bin/webgbrowse/configureTracks and /usr/lib/cgi-bin/webgbrowse/generateConfigurationData2.0 files like /etc/gbrowse2/225c87610282ae0c1575dfb7e22bb640.conf are supposedly created. Maybe you could provide me insight on that?

Thank you very much for taking the time to attending to my little inquiry.

Cheers,
--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
<a href="tel:%2B63-49-536-2701%20extension%202643" value="+63495362701" target="_blank">+63-49-536-2701 extension 2643

<a href="tel:%2B639183981185" value="+639183981185" target="_blank">+639183981185

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone except as permitted by the author sender.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



Cheers,
--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone except as permitted by the author sender.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Loading...